Heritable variation in gene expression is the key to maximizing genetic gain and preserving genetic diversity with a properly designed breeding program.

Abstract

A hierarchical organization of molecular phenotypes provides a biological system of genes and pathways which can lead to different genotypes (redundancy) being selected in different subpopulations for the same phenotype. Heritable variation in transcription and translation is the key driver of genetic change. Redundancy in the regulatory code allows for genetic diversity amongst subpopulations. Gene expression is regulated by transcription factors (TF) ensuring that the right genes are active in the right tissue at the right time. A large amount of standing genetic variation is available from the many potential TF-TF interactions and TF interactions with other regulatory elements. Further diversity is possible in that each TF can target hundreds to thousands of different genes; and many of these genes through exon splicing, can produce functionally diverse transcripts and protein isoforms. These complex interactions form gene regulatory networks controlling specialized metabolic pathways. Which pathway is enriched is dependent upon the epistasis created by different founders, i.e., the ancestral makeup of the subpopulation. Selection on these epistatic effects leads to gametic disequilibrium between replicate populations causing them to differentiate. Different genetic architecture results in varied allele frequencies between subpopulations and intermediary allele frequencies in the global population. Genetic diversity within the Holstein breed can be preserved or increased with a proper population structure. This includes having multiple lines of Holsteins; utilizing multiple reference and target populations; genomic predictions for an overall global population and each separate subpopulation; avoidance of pooling SNPs; and analysis of transcriptomes for possible grouping of animals.